Starting phenix.real_space_refine on Thu Jul 18 20:12:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/07_2024/8u3f_41860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/07_2024/8u3f_41860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/07_2024/8u3f_41860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/07_2024/8u3f_41860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/07_2024/8u3f_41860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3f_41860/07_2024/8u3f_41860.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2274 2.51 5 N 534 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3410 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 19, 'TRANS': 417} Chain breaks: 2 Time building chain proxies: 2.87, per 1000 atoms: 0.84 Number of scatterers: 3410 At special positions: 0 Unit cell: (58.1, 64.74, 86.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 585 8.00 N 534 7.00 C 2274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 387 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 598.7 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.555A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.635A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.506A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Proline residue: A 215 - end of helix removed outlier: 3.712A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.648A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 311 removed outlier: 3.743A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 359 through 384 Proline residue: A 375 - end of helix removed outlier: 3.614A pdb=" N GLY A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.636A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.712A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 920 1.46 - 1.58: 1565 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3513 Sorted by residual: bond pdb=" CA VAL A 280 " pdb=" CB VAL A 280 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.50e-01 bond pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 1.469 1.476 -0.007 7.40e-03 1.83e+04 9.44e-01 bond pdb=" CA ASN A 323 " pdb=" C ASN A 323 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.66e-01 bond pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 1.447 1.457 -0.011 1.18e-02 7.18e+03 8.22e-01 bond pdb=" CB VAL A 211 " pdb=" CG2 VAL A 211 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.47e-01 ... (remaining 3508 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.61: 105 106.61 - 113.48: 1913 113.48 - 120.34: 1428 120.34 - 127.20: 1292 127.20 - 134.06: 53 Bond angle restraints: 4791 Sorted by residual: angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 109.34 113.83 -4.49 2.08e+00 2.31e-01 4.66e+00 angle pdb=" C LEU A 447 " pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 122.89 120.51 2.38 1.12e+00 7.97e-01 4.51e+00 angle pdb=" CA THR A 153 " pdb=" C THR A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 118.44 121.64 -3.20 1.59e+00 3.96e-01 4.05e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 109.34 113.48 -4.14 2.08e+00 2.31e-01 3.97e+00 angle pdb=" CA LEU A 289 " pdb=" C LEU A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 118.44 121.58 -3.14 1.59e+00 3.96e-01 3.91e+00 ... (remaining 4786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1771 16.48 - 32.95: 182 32.95 - 49.43: 30 49.43 - 65.90: 3 65.90 - 82.38: 1 Dihedral angle restraints: 1987 sinusoidal: 737 harmonic: 1250 Sorted by residual: dihedral pdb=" CA ASN A 323 " pdb=" C ASN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASN A 323 " pdb=" CB ASN A 323 " pdb=" CG ASN A 323 " pdb=" OD1 ASN A 323 " ideal model delta sinusoidal sigma weight residual -90.00 -152.99 62.99 2 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CG LYS A 278 " pdb=" CD LYS A 278 " pdb=" CE LYS A 278 " pdb=" NZ LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -136.68 -43.32 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 1984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 356 0.037 - 0.073: 148 0.073 - 0.110: 33 0.110 - 0.146: 6 0.146 - 0.183: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA PRO A 192 " pdb=" N PRO A 192 " pdb=" C PRO A 192 " pdb=" CB PRO A 192 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 541 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " 0.014 2.00e-02 2.50e+03 1.40e-02 3.45e+00 pdb=" CG PHE A 305 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 290 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 163 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.022 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 911 2.79 - 3.32: 3343 3.32 - 3.85: 5797 3.85 - 4.37: 6821 4.37 - 4.90: 11982 Nonbonded interactions: 28854 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OE2 GLU A 175 " model vdw 2.265 2.520 nonbonded pdb=" OH TYR A 101 " pdb=" OD1 ASP A 158 " model vdw 2.286 2.440 nonbonded pdb=" O PRO A 192 " pdb=" NH2 ARG A 353 " model vdw 2.314 2.520 nonbonded pdb=" OG SER A 37 " pdb=" OE2 GLU A 262 " model vdw 2.352 2.440 nonbonded pdb=" O ALA A 444 " pdb=" OG1 THR A 448 " model vdw 2.358 2.440 ... (remaining 28849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3513 Z= 0.299 Angle : 0.625 5.254 4791 Z= 0.369 Chirality : 0.041 0.183 544 Planarity : 0.005 0.046 581 Dihedral : 12.988 82.377 1188 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.37), residues: 431 helix: -0.90 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.006 0.001 HIS A 298 PHE 0.032 0.002 PHE A 305 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.366 Fit side-chains REVERT: A 256 LYS cc_start: 0.5750 (mmtt) cc_final: 0.4278 (tttp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1768 time to fit residues: 9.1844 Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3513 Z= 0.203 Angle : 0.542 5.383 4791 Z= 0.286 Chirality : 0.040 0.117 544 Planarity : 0.005 0.045 581 Dihedral : 4.241 20.644 463 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 10.53 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.40), residues: 431 helix: 0.54 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -1.11 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.012 0.001 PHE A 305 TYR 0.011 0.001 TYR A 306 ARG 0.002 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.357 Fit side-chains REVERT: A 256 LYS cc_start: 0.5688 (mmtt) cc_final: 0.4242 (tttp) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.1802 time to fit residues: 8.3001 Evaluate side-chains 34 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3513 Z= 0.217 Angle : 0.539 5.246 4791 Z= 0.280 Chirality : 0.040 0.114 544 Planarity : 0.005 0.042 581 Dihedral : 4.218 22.843 463 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 13.30 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.40), residues: 431 helix: 1.12 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.08 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.351 Fit side-chains REVERT: A 256 LYS cc_start: 0.5722 (mmtt) cc_final: 0.4223 (tttp) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.1790 time to fit residues: 8.2468 Evaluate side-chains 36 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3513 Z= 0.183 Angle : 0.518 5.234 4791 Z= 0.267 Chirality : 0.039 0.113 544 Planarity : 0.005 0.041 581 Dihedral : 4.161 22.795 463 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 13.57 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.41), residues: 431 helix: 1.48 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.90 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.014 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.000 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.365 Fit side-chains REVERT: A 256 LYS cc_start: 0.5658 (mmtt) cc_final: 0.4154 (tttp) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.1480 time to fit residues: 7.5160 Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3513 Z= 0.204 Angle : 0.524 5.232 4791 Z= 0.270 Chirality : 0.040 0.114 544 Planarity : 0.005 0.042 581 Dihedral : 4.134 22.983 463 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 14.40 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.41), residues: 431 helix: 1.60 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.78 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.001 PHE A 51 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.345 Fit side-chains REVERT: A 256 LYS cc_start: 0.5719 (mmtt) cc_final: 0.4158 (tttp) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.1499 time to fit residues: 7.4419 Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3513 Z= 0.225 Angle : 0.534 5.240 4791 Z= 0.275 Chirality : 0.040 0.116 544 Planarity : 0.005 0.043 581 Dihedral : 4.139 22.880 463 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 14.68 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.41), residues: 431 helix: 1.64 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.76 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.013 0.001 PHE A 51 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.361 Fit side-chains REVERT: A 256 LYS cc_start: 0.5747 (mmtt) cc_final: 0.4155 (tttp) outliers start: 9 outliers final: 9 residues processed: 37 average time/residue: 0.1472 time to fit residues: 7.1294 Evaluate side-chains 41 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 446 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.0270 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3513 Z= 0.154 Angle : 0.506 5.201 4791 Z= 0.259 Chirality : 0.039 0.111 544 Planarity : 0.005 0.042 581 Dihedral : 4.046 23.257 463 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 14.40 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.41), residues: 431 helix: 1.76 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -0.66 (0.63), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.013 0.001 PHE A 51 TYR 0.010 0.001 TYR A 306 ARG 0.000 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.5714 (mmtt) cc_final: 0.4142 (tttp) REVERT: A 257 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7684 (ttm110) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.1447 time to fit residues: 7.2099 Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.0070 chunk 30 optimal weight: 0.3980 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3513 Z= 0.144 Angle : 0.497 5.181 4791 Z= 0.255 Chirality : 0.038 0.114 544 Planarity : 0.005 0.043 581 Dihedral : 4.006 23.216 463 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 14.68 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.41), residues: 431 helix: 2.00 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.62 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.013 0.001 PHE A 51 TYR 0.010 0.001 TYR A 306 ARG 0.000 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.5672 (mmtt) cc_final: 0.4085 (tttp) REVERT: A 257 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7691 (ttm110) outliers start: 9 outliers final: 8 residues processed: 39 average time/residue: 0.1723 time to fit residues: 8.5317 Evaluate side-chains 38 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 446 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3513 Z= 0.200 Angle : 0.520 5.194 4791 Z= 0.268 Chirality : 0.040 0.118 544 Planarity : 0.005 0.043 581 Dihedral : 4.054 23.369 463 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 15.24 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.41), residues: 431 helix: 1.81 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -0.55 (0.63), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.014 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.5740 (mmtt) cc_final: 0.4116 (tttp) REVERT: A 257 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7719 (ttm110) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.1455 time to fit residues: 7.4015 Evaluate side-chains 42 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3513 Z= 0.158 Angle : 0.505 5.191 4791 Z= 0.259 Chirality : 0.039 0.122 544 Planarity : 0.005 0.043 581 Dihedral : 4.018 23.209 463 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 15.24 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.41), residues: 431 helix: 2.01 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.54 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.013 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.000 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.5730 (mmtt) cc_final: 0.4127 (tttp) REVERT: A 257 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7702 (ttm110) outliers start: 9 outliers final: 9 residues processed: 37 average time/residue: 0.1661 time to fit residues: 7.7197 Evaluate side-chains 40 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103893 restraints weight = 3841.761| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.72 r_work: 0.3023 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3513 Z= 0.208 Angle : 0.522 5.206 4791 Z= 0.269 Chirality : 0.040 0.127 544 Planarity : 0.005 0.043 581 Dihedral : 4.063 23.315 463 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 15.51 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.41), residues: 431 helix: 1.84 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -0.55 (0.63), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.002 0.001 HIS A 414 PHE 0.013 0.001 PHE A 51 TYR 0.009 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1134.83 seconds wall clock time: 21 minutes 13.55 seconds (1273.55 seconds total)